The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis

PLoS Genet. 2019 Aug 12;15(8):e1008328. doi: 10.1371/journal.pgen.1008328. eCollection 2019 Aug.

Abstract

TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms. In Archaea, TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however, its biological significance and functional mechanism remain unknown. This work demonstrated that TRAM0076 is an abundant standalone TRAM protein in the genetically tractable methanoarcheaon Methanococcus maripaludis. Deletion of MMP0076, the gene encoding TRAM0076, markedly reduced the growth and altered transcription of 55% of the genome. Substitution mutations of Phe39, Phe42, Phe63, Phe65 and Arg35 in the recombinant TRAM0076 decreased the in vitro duplex RNA unfolding activity. These mutations also prevented complementation of the growth defect of the MMP0076 deletion mutant, indicating that the duplex RNA unfolding activity was essential for its physiological function. A genome-wide mapping of transcription start sites identified many 5' untranslated regions (5'UTRs) of 20-60 nt which could be potential targets of a RNA chaperone. TRAM0076 unfolded three representative 5'UTR structures in vitro and facilitated the in vivo expression of a mCherry reporter system fused to the 5'UTRs, thus behaving like a transcription anti-terminator. Flag-tagged-TRAM0076 co-immunoprecipitated a large number of cellular RNAs, suggesting that TRAM0076 plays multiple roles in addition to unfolding incorrect RNA structures. This work demonstrates that the conserved archaeal RNA chaperone TRAM globally affects gene expression and may represent a transcriptional element in ancient life of the RNA world.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions / genetics
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism*
  • Genome, Archaeal / genetics
  • Methanococcus / physiology*
  • Molecular Chaperones / genetics
  • Molecular Chaperones / metabolism*
  • RNA, Archaeal / metabolism*
  • Transcription, Genetic
  • Transcriptome / genetics

Substances

  • 5' Untranslated Regions
  • Archaeal Proteins
  • Molecular Chaperones
  • RNA, Archaeal

Grants and funding

Funding was provided by the National Natural Science foundation of China (http://www.nsfc.gov.cn/) under grant no. 31430001 (X.D), 91751203 (X.D) and 31670049 (J.L), and by Ministry of Science and Technology, China (www.most.gov.cn) under grant no. 2018YFC0310801 (X.D). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.